If you free Shadowhearth in the ship and let her manipulate the ship at the end and trigger the cutscene with her instead of the main character, shadowheart will be missing at the beach. Not lying there for you and neither will be at the door. Hope this helps.
That happened in my very first attempt - I could HEAR her ("does this thing even open?" etc - talking about the artifact) but she was absolutely nowhere to be found. I went back and scoured the whole area about 5 times. Then I got my ass handed to me by the 3 Intellect Devourers and had to reload, and there she was next to me on the beach.